1 Overview

Data

Normalization

Model options

Network processing

cor/cov method: pearson

2 Load and normalize data

Data

Normalization

2.1 Load TCGA data

See prepare.tcga.survival.data function for how to configure parameters.

This uses data packages from obtained from ‘github:averissimo/tcga’ that contain FPKM expression levels.

prepare.tcga.survival.data('luad.data.2018.10.17',
                           'primary.solid.tumor',
                            normalization        = 'center',
                            log2.pre.normalize   = TRUE,
                            handle.duplicates    = 'keep_first',
                            coding.genes         = TRUE,
                            subtract.surv.column = '')

2.1.1 Summary of data

## [INFO]        Loaded data from TCGA: luad.data.2018.10.17
## [INFO]               type of tissue: primary.solid.tumor
## [INFO]   observations (individuals): 451 (162 event / 289 censored)
## [INFO]            variables (genes): 19861

2.1.2 Survival curve

2.2 Load degree data

Network processing

  • Degree calculation: string
  • Edge cutoff: 0
  • Unweighted edges

cor/cov method: pearson

  • only applies if network type is correlation/covariance

2.3 Preparing degree vector

  • Normalize degree between 0 and 1
  • Hub: heuristic( 1 - degree )
  • Orphan: heuristic( degree )
  • trans.fun is a double power to scale the values

see ?glmSparseNet::heuristicScale or ?glmSparseNet::hubHeuristic

# see ?glmSparseNet::heuristic.scale
trans.fun <- function(x) {
    heuristicScale(x) + 0.2
}

2.3.1 Genes with degree above 4000

ensembl_gene_id degree external_gene_name
ENSG00000150991 10394 UBC
ENSG00000170325 6346 PRDM10
ENSG00000100300 5797 TSPO
ENSG00000174775 5614 HRAS
ENSG00000142208 5573 AKT1
ENSG00000111640 5363 GAPDH
ENSG00000163631 5260 ALB
ENSG00000177606 4952 JUN
ENSG00000141510 4936 TP53
ENSG00000197122 4903 SRC
ENSG00000254647 4592 INS
ENSG00000112062 4187 MAPK14
ENSG00000170315 4114 UBB
ENSG00000170345 4010 FOS

2.3.2 Original degree frequency

Original

LOG10 Scale on X-axis

3 Model Inference

3.1 Train and test sets

## [INFO] Size of sets: (size/events)
##  * Train: 80.00% ::  360 /  129
##  *  Test: 20.00% ::   91 /  33
## [INFO] Number of variables per model:
Model BaseModel Alpha TargetVars nvars
Elastic Net Elastic Net 0.10 110 117
Hub Elastic Net 0.10 110 110
Orphan Elastic Net 0.10 110 112
Elastic Net Hub 0.10 56 60
Hub Hub 0.10 56 56
Orphan Hub 0.10 56 66
Elastic Net Orphan 0.10 97 97
Hub Orphan 0.10 97 97
Orphan Orphan 0.10 97 99 
## [INFO] note, selected variables could be slightly different from target, to have more accuracy increase nlambda in code

4 Results

4.1 Relative risk distribution

Calculated using the inferred models and the train/test datasets. The higher the better.

Test Set

Train Set

4.2 Kaplan-Meier Curves

4.2.1 Models on test sets

Elastic Net (base model: Elastic Net)

Test set

Training set

Hub (base model: Elastic Net)

Test set

Training set

Orphan (base model: Elastic Net)

Test set

Training set

Elastic Net (base model: Hub)

Test set

Training set

Hub (base model: Hub)

Test set

Training set

Orphan (base model: Hub)

Test set

Training set

Elastic Net (base model: Orphan)

Test set

Training set

Hub (base model: Orphan)

Test set

Training set

Orphan (base model: Orphan)

Test set

Training set

4.3 Summary Table

weighted penalization project tissue cutoff coding.genes alpha model nvars km.train km.test c.index.train c.index.test
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Elastic Net 117 0 0.0028686 0.7849739 0.6852922
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Hub 110 0 0.0773024 0.7977132 0.6416185
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Orphan 112 0 0.0300240 0.7941130 0.6339114
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Elastic Net 60 0 0.0020476 0.7492087 0.7052023
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Hub 56 0 0.0240581 0.7464789 0.6602441
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Orphan 66 0 0.0511146 0.7410191 0.6435453
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Elastic Net 97 0 0.0020476 0.7680804 0.6974952
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Hub 97 0 0.0773024 0.7881389 0.6429030
FALSE string luad.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Orphan 99 0 0.0131315 0.7837870 0.6345536

4.4 Non-zero genes

4.4.1 Venn Diagram of selected genes

4.4.1.1 Overlap between models (with same target number of variables)

Base model: Elastic Net with Target Vars: 110 and Alpha: 0.10

Base model: Hub with Target Vars: 56 and Alpha: 0.10

Base model: Orphan with Target Vars: 97 and Alpha: 0.10

Table of genes in models

(not running at the moment)

5 5000 Runs

5.1 C-Index distribution

Test set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Test set) Hub Elastic Net 110 0.10 0.617 0.050 0.617 0.431
C-Index (Test set) Hub Hub 56 0.10 0.623 0.051 0.624 0.418
C-Index (Test set) Hub Orphan 97 0.10 0.619 0.050 0.620 0.43
C-Index (Test set) Elastic Net Elastic Net 110 0.10 0.620 0.050 0.621 0.436
C-Index (Test set) Elastic Net Hub 56 0.10 0.624 0.050 0.625 0.449
C-Index (Test set) Elastic Net Orphan 97 0.10 0.621 0.050 0.621 0.443
C-Index (Test set) Orphan Elastic Net 110 0.10 0.606 0.050 0.607 0.413
C-Index (Test set) Orphan Hub 56 0.10 0.603 0.050 0.604 0.422
C-Index (Test set) Orphan Orphan 97 0.10 0.606 0.050 0.607 0.413
Log-rank (Test set) Hub Elastic Net 110 0.10 0.247 0.263 0.144 4.95e-07
Log-rank (Test set) Hub Hub 56 0.10 0.239 0.261 0.134 7.82e-07
Log-rank (Test set) Hub Orphan 97 0.10 0.237 0.257 0.138 6.26e-06
Log-rank (Test set) Elastic Net Elastic Net 110 0.10 0.253 0.266 0.146 9.45e-06
Log-rank (Test set) Elastic Net Hub 56 0.10 0.228 0.253 0.123 7.67e-06
Log-rank (Test set) Elastic Net Orphan 97 0.10 0.250 0.264 0.144 8.72e-07
Log-rank (Test set) Orphan Elastic Net 110 0.10 0.277 0.275 0.172 5.51e-06
Log-rank (Test set) Orphan Hub 56 0.10 0.288 0.278 0.185 2.37e-06
Log-rank (Test set) Orphan Orphan 97 0.10 0.278 0.274 0.175 5.51e-06

C-Index Distribution

Rank

Elastic Net vs Hub
base.model r.squared
Elastic Net with target nvars: 110 alpha: 0.10 0.6616546
Hub with target nvars: 56 alpha: 0.10 0.6473246
Orphan with target nvars: 97 alpha: 0.10 0.6624709

Elastic Net vs. Orphan
base.model r.squared
Elastic Net with target nvars: 110 alpha: 0.10 0.8904119
Hub with target nvars: 56 alpha: 0.10 0.8616601
Orphan with target nvars: 97 alpha: 0.10 0.8879366

Hub vs. Orphan
base.model r.squared
Elastic Net with target nvars: 110 alpha: 0.10 0.6262076
Hub with target nvars: 56 alpha: 0.10 0.6196455
Orphan with target nvars: 97 alpha: 0.10 0.6305587

Train set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Train set) Hub Elastic Net 110 0.10 0.785 0.011 0.785 0.746
C-Index (Train set) Hub Hub 56 0.10 0.733 0.012 0.733 0.689
C-Index (Train set) Hub Orphan 97 0.10 0.774 0.011 0.774 0.735
C-Index (Train set) Elastic Net Elastic Net 110 0.10 0.781 0.011 0.781 0.745
C-Index (Train set) Elastic Net Hub 56 0.10 0.738 0.010 0.738 0.705
C-Index (Train set) Elastic Net Orphan 97 0.10 0.771 0.011 0.771 0.734
C-Index (Train set) Orphan Elastic Net 110 0.10 0.784 0.011 0.784 0.744
C-Index (Train set) Orphan Hub 56 0.10 0.735 0.011 0.735 0.696
C-Index (Train set) Orphan Orphan 97 0.10 0.772 0.012 0.772 0.735
Log-rank (Train set) Hub Elastic Net 110 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Hub Hub 56 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Hub Orphan 97 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Elastic Net 110 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Hub 56 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Orphan 97 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Elastic Net 110 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Hub 56 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Orphan 97 0.10 0.000 0.000 0.000 0

C-Index Distribution

C-Index Rank

5.2 Log-rank test on Kaplan-Meier models

5.2.1 Log-Rank distribution

Cumulative

Distribution of Log-rank test with groups separated by high and low risk groups

Distribution

Distribution of Log-rank test with groups separated by high and low risk groups

5.2.2 Log-Rank Rank

5.2.2.1 Elastic Net vs Hub

base.model r.squared
Elastic Net with target nvars: 110 alpha: 0.10 0.2454922
Hub with target nvars: 56 alpha: 0.10 0.2551984
Orphan with target nvars: 97 alpha: 0.10 0.2470694

5.2.2.2 Elastic Net vs. Orphan

base.model r.squared
Elastic Net with target nvars: 110 alpha: 0.10 0.4486532
Hub with target nvars: 56 alpha: 0.10 0.4108992
Orphan with target nvars: 97 alpha: 0.10 0.4531178

5.2.2.3 Hub vs. Orphan

base.model r.squared
Elastic Net with target nvars: 110 alpha: 0.10 0.2242910
Hub with target nvars: 56 alpha: 0.10 0.2246238
Orphan with target nvars: 97 alpha: 0.10 0.2303688

5.3 Consesus genes

5.3.1 Selected genes over all runs

Bar plots of frequencies

Overlap between variables selected

Base model: Elastic Net with Target Vars: 110 and Alpha: 0.10

Base model: Hub with Target Vars: 56 and Alpha: 0.10

Base model: Orphan with Target Vars: 97 and Alpha: 0.10

5.3.2 Selected genes in significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Bar plots of frequencies

Overlap between variables selected

5.3.2.0.1 Base model Elastic Net with target nvars: 0.10 alpha: 110

5.3.2.0.2 Base model Hub with target nvars: 0.10 alpha: 56

5.3.2.0.3 Base model Orphan with target nvars: 0.10 alpha: 97

5.3.3 Genes in Significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Top consensus 20 genes

Gene Overlap total
PITX3 2 8194
VAX1 3 7850
RHOV 2 7637
RHOF 2 6870
PLEKHB1 2 6322
ABAT 3 6055
PRKCD 2 5877
CLEC17A 2 5725
STAP1 2 5667
MELTF 2 5655
SPANXA1 3 5571
FAM83A 2 5401
HSPA4 2 5371
RHOQ 2 5354
NOS3 2 5311
BEX4 2 5242
MYLIP 2 5131
C1QTNF6 2 5112
GNG7 2 4934
LDLRAD3 2 4806

All Genes

PITX3(8194), VAX1(7850), RHOV(7637), RHOF(6870), PLEKHB1(6322), ABAT(6055), PRKCD(5877), CLEC17A(5725), STAP1(5667), MELTF(5655), SPANXA1(5571), FAM83A(5401), HSPA4(5371), RHOQ(5354), NOS3(5311), BEX4(5242), MYLIP(5131), C1QTNF6(5112), GNG7(4934), LDLRAD3(4806), BTN2A2(4792), DKK1(4731), ZFAND4(4706), MAPK13(4652), CRYGD(4645), GAPDH(4590), PRKACB(4567), AKT1S1(4567), ABL1(4536), PLEKHA8P1(4534), CD200R1L(4526), TLE1(4500), CPS1(4494), DTNBP1(4466), NRAS(4451), ACTC1(4420), TSPO(4415), UBC(4390), INAFM2(4382), FURIN(4375), LCK(4239), KRT6A(4216), SLC46A3(4182), ZNF479(4162), CCDC181(4075), PSKH2(4034), IER5L(3993), DECR1(3982), TMEM130(3979), SAMD13(3958), FYN(3949), INSR(3905), PIK3CG(3895), KRAS(3890), HSDL1(3880), CDC42(3801), RRAS(3793), KIR3DL2(3761), RUBCNL(3738), ABCC2(3715), TNF(3631), KLHDC8B(3615), CCDC149(3585), FMO3(3583), CLEC20A(3565), LCE5A(3553), PRDM10(3536), PRKCA(3528), UMPS(3521), MAPK11(3484), STIMATE(3391), E2F7(3379), KIT(3379), MSLNL(3374), INS(3367), FLNC(3340), LOXL2(3319), FUT4(3310), CDK15(3308), C18orf54(3290), CALB2(3266), CIDEC(3265), ENPP5(3264), GATA4(3245), EEF1E1-BLOC1S5(3236), MSANTD3-TMEFF1(3235), EPHX1(3233), GLI2(3229), AKT1(3195), RPS6KA1(3191), MYO6(3128), TNS4(3053), GSK3A(3031), OASL(3008), UBL4B(2973), PLCD3(2950), EMC6(2923), KIR2DL1(2911), NLRP5(2902), ANKRD65(2885), UCN2(2867), ITGA2(2858), RPS6KL1(2823), F2(2783), FAM210B(2779), RCVRN(2778), HRAS(2766), OAS2(2722), GOLGA6D(2710), GATD3B(2700), ACTA1(2674), TP53(2661), TYRO3(2649), EGFR(2583), CDKAL1(2567), RAD23B(2524), LDLRAD3(2480), OR14C36(2479), LCE1D(2474), ZC3H12D(2473), ACTBL2(2459), ALB(2447), USP4(2432), PPP3CC(2414), LINGO2(2387), IRX5(2383), POTEJ(2368), KCNV1(2367), ZNF165(2366), TSPY3(2355), C19orf48(2348), EHMT2(2340), PPP1R13B(2325), SRC(2319), KYNU(2314), CPXM2(2314), GGACT(2265), ENSG00000270168(2256), KRT38(2245), ANKRD53(2242), TM4SF19(2238), GJB3(2225), RASSF10(2225), MGAT5B(2203), ANGPTL4(2183), MAPK4(2175), VEGFC(2175), CDK4(2167), RAB11A(2164), VDAC1(2127), SLC4A8(2097), PTPRH(2092), TSPAN11(2069), IGF2BP1(2055), RAMACL(2046), TCP10L2(1995), RIPK4(1994), RAC1(1993), PPP3CA(1982), CDY2B(1981), AP000311.1(1967), ACTR1B(1961), FGFR1(1954), ACTRT3(1947), GOLGA6D(1945), ANO4(1934), NTSR1(1928), AP000311.1(1925), MCM5(1916), CCL3L3(1915), GALNT2(1906), MRAS(1890), ST13(1889), KRTAP7-1(1880), AC245033.1(1861), CDK1(1858), ZNF750(1831), GLCCI1(1829), DTNBP1(1824), CALM3(1822), HSPA8(1808), HOXA13(1799), MAPK7(1799), OAS3(1797), VEGFA(1794), UPK1B(1745), RHOH(1741), AC011452.1(1736), ADM(1722), AC010325.1(1688), NEIL3(1686), TMEM171(1686), MYC(1686), APOC4-APOC2(1684), SEPTIN2(1683), ATF7IP2(1662), CDIN1(1642), TMEM215(1639), TPGS1(1635), NFKB1(1634), STK11(1626), ACTR3B(1623), SMAD3(1611), TOMM34(1604), AKT2(1575), MESD(1569), TSPY1(1555), LATS2(1547), TRIM6(1541), CIDEB(1540), NLRP8(1525), HLA-DOB(1525), INSL4(1517), HERPUD1(1516), AHSG(1516), PRAMEF1(1510), C5AR2(1507), PRKCG(1507), ZDHHC11B(1502), STOX1(1499), FDXACB1(1496), MARCHF4(1495), MAPK1(1494), JUN(1492), PRORY(1480), RHCG(1479), HLA-DMA(1474), TMEM25(1448), CA5B(1420), UBL4B(1415), HPF1(1412), FHAD1(1412), MAGEA5(1404), MAPK12(1401), UBB(1400), CFTR(1396), WWC2-AS2(1390), IRX2(1372), GNPNAT1(1368), KIR3DL2(1366), ZNF502(1363), AQP8(1357), PLEK2(1350), TCTA(1347), ISCU(1338), OR7E47P(1337), SFTA3(1328), BEST4(1326), TOPAZ1(1318), CATSPERE(1318), STK11(1302), CALN1(1300), CD79A(1297), MSANTD3(1290), CSNK1E(1290), TMEM256-PLSCR3(1284), BCRP2(1283), MUC2(1280), USP4(1275), EPHX1(1270), CCT6A(1270), WT1(1264), SLC47A1(1257), SNN(1249), MACO1(1241), UCK2(1239), C22orf46(1238), UBL4A(1238), TEX26(1235), RHOXF2(1219), CALM2(1209), ACTA1(1196), BEX5(1184), TFDP1(1181), SIX5(1176), FIBCD1(1174), UBD(1173), WARS2(1165), WNT1(1157), IRX5(1152), RAC1(1144), ENO3(1143), IKZF4(1133), INPP5A(1117), CD8B2(1108), MAPK4(1103), C3orf18(1101), CTNNB1(1100), TTC24(1099), SSX2B(1096), IGF2BP1(1091), KLF14(1090), LDHA(1088), MAPRE3(1086), RPS6KB2(1082), EPHB2(1075), ANP32A(1073), AMDHD1(1069), TERT(1069), GPD1L(1066), FDCSP(1060), FRZB(1053), C11orf16(1046), PHLPP1(1042), GALNT11(1041), PSTPIP2(1037), TRIM39(1036), ACTL6B(1036), INO80B-WBP1(1025), FAM117A(1023), MTMR12(1023), CDH1(1021), MAPK14(1021), GMPS(1018), NPAP1L(1018), C20orf141(1015), DNAJC28(1010), C1orf141(1005), AC005726.1(997), MAPK7(996), ACAT2(992), RHOH(979), SAMM50(977), AKTIP(977), AKAP12(974), UNC5D(971), MAPK3(965), AP3S1(961), CXorf21(960), C6orf62(959), JOSD1(951), ACSM5(945), IGFBP1(944), VSTM2A(942), HDAC4(942), MET(939), ACTB(937), FAM184A(935), YES1(921), STK33(918), NPAS2(915), GDPD2(913), CLDN16(913), KRT81(906), SMS(903), WFDC3(896), TCN1(890), PRKAR1A(887), GCG(886), GUCA2B(880), KLK8(879), YWHAE(879), SPATA22(873), KBTBD8(873), NINJ2(865), SEC61G(859), SPDL1(856), ACTL7B(856), LCE1D(854), CPA5(847), FAM76A(844), ENSG00000278500(833), CCDC184(833), TNNT1(830), OR10Z1(828), B3GALT1(823), LANCL2(820), HLA-DQB2(819), FUCA1(817), FBN2(812), CERS4(809), ARL4D(808), EPN1(807), C7orf77(806), TXNDC11(804), ACSBG1(803), BAIAP2L2(799), FRRS1(796), PEBP1(795), CSNK2A2(794), KRTAP11-1(792), FGF12(790), FGF2(790), CCR2(783), RHOA(781), CERS4(776), BMP15(776), NLRP5(767), NOTCH1(764), ARG2(762), DNER(757), AC005697.1(757), OR10Z1(755), TOR4A(754), TM6SF1(752), MYH14(752), OSR1(745), GDPD2(743), SMG9(739), RHOD(736), MTURN(736), HSPA2(734), PIM2(733), CABP2(728), LINC00324(720), BTN2A1(717), HDAC5(716), PSMD2(716), FAM9C(713), CDKN2A(708), AC233723.1(707), CTSL(703), HDAC9(702), ANK2(699), TK2(697), CD8A(688), ADM(687), ECT2(685), MYO18B(683), TDRD1(681), SHC1(681), PSMB7(681), HRH3(678), TMEM81(672), ZP2(671), FOS(669), TMEM44(661), ANGPTL4(661), GPR78(660), CERS4(659), TMEM50B(656), DMC1(655), ENSG00000260300(652), CRYGD(651), CERKL(649), CMTM7(648), NRG4(648), POLR1G(647), SERBP1(641), CLEC18A(641), PPP1R21(639), LRIG1(638), ACTA2(636), FSCN1(635), PRKX(635), DENND1C(633), CDC42EP2(630), XXYLT1(630), RPS4Y2(627), LYN(627), YWHAG(626), PPP1R3G(624), HSP90AB1(624), ORMDL3(623), GRIK2(620), UTS2(612), DEDD2(610), RAC3(610), TRIM38(607), KIR2DL1(607), BCAN(607), GABRG1(601), LYPD3(594), ACTR10(586), C11orf52(583), CCT2(579), FKBP4(577), CIDEA(575), F8A2(573), EPHA6(571), GOLPH3(570), RIT2(570), ADH4(569), CDX2(568), UGT2B11(564), SMOX(561), ACO2(561), ENSG00000255863(558), ARG2(555), AURKC(552), RAB25(552), SIRT1(551), PRKAG2(548), CR2(548), TRIM28(545), LETM2(545), LURAP1(540), LILRA4(534), ZBTB18(532), DIRAS1(530), OAS1(529), EGR2(527), TFAP2A(527), DUX4L9(527), OR1F1(524), ACSM5(524), HRCT1(517), ZFP3(517), PCSK9(516), ARL14(511), OR2J3(508), SPIN4(501), FAM207A(500), NXNL2(495), HSP90AA1(495), XRCC6(491), IFNE(489), NPY5R(488), MTHFS(487), ADCY10(482), CA2(480), HSPA9(479), CHCHD4(479), FOXB1(479), ADCY2(475), SLC35G2(473), CDIP1(471), HDAC1(471), LDHA(470), BTK(468), AC069257.3(466), GATA3(466), XAGE1B(464), HSPA2(461), BPIFB1(459), YWHAZ(458), PZP(457), EPHA5(456), NEUROD1(455), TUBAL3(455), TGFB1(453), SDK1(449), PXK(447), ACCSL(446), ISL2(445), C12orf76(444), ACSL3(441), LRP10(441), EFCAB8(441), RRAD(441), TF(438), POTEI(438), LEF1(437), ACTRT1(436), FAM72B(435), MZT2A(433), TTC32(427), MEAF6(425), NFKBIA(425), C1orf94(424), MAPK12(424), DSG2(423), MKKS(421), OR2A7(420), FGF8(420), C2orf42(419), GJA5(419), CPA2(415), RGS20(415), PPIAL4A(414), BCL2L10(411), KLF10(410), RPE65(409), PRAMEF2(409), ENOX1(407), LY6K(407), OPA3(406), XCR1(405), STK32A(405), OLFM1(404), FBXO31(403), FAM43B(403), PRKN(403), RRAS2(402), FAM131C(401), ACTG1(400), TMEM241(399), FUT1(399), SDCBP2(397), C1QL2(395), B4GALT6(394), ACSL3(393), ZIC5(393), ZSCAN26(393), NPB(392), TP53I3(390), RPE65(389), C15orf56(388), ACTL8(388), PFKP(383), C7orf69(381), FBXL21P(380), PLXND1(379), ASB3(378), FAIM2(378), POPDC3(377), DNAJB4(377), HSPA6(377), NXPE2(377), TBP(376), CYP17A1(373), DRP2(371), ADA2(370), CREG2(369), DMRTC1(368), PELI1(365), CDK2(363), CASP14(361), MEGF8(361), SST(361), CAMTA1(360), NPAS1(359), AP2M1(359), CALM1(358), GTF3C6(357), CDH17(356), INGX(356), GCK(355), SQLE(353), LGR5(353), LRFN4(353), TTC16(352), CNMD(351), OR2A7(351), YWHAH(351), BTBD9(350), FXYD2(349), CDCP1(345), TMA16(345), CAT(344), ANKUB1(343), KIR2DP1(342), BCL2L1(342), PITPNC1(341), RND3(341), LRRC66(339), PRAMEF14(339), SARAF(336), RHOC(335), TFEB(334), SPANXD(334), SPATA7(333), KDM8(333), EPHA1(333), BCL2(332), PHF1(331), SST(331), PPP1R1C(330), GNAO1(329), AKTIP(328), AC245033.1(326), ANLN(323), TAS1R2(321), CCDC88C(318), PTCHD4(315), STX3(315), GRWD1(313), COX7B2(312), ASCL3(311), NGEF(311), PPEF1(310), GAK(309), LRRC3B(307), GUCA1C(306), ANO3(305), PRR30(305), ECT2L(305), FAM83D(304), CTSL(304), STK17B(303), VWA2(302), CDKN1B(302), TYMS(302), KRT38(301), TMEM11(300), JAK1(299), TRPA1(298), PLEKHG3(298), ZNF77(298), PPP5C(295), NUMBL(295), ANKRD13A(294), TMEM52B(294), KIR2DL3(293), NPC2(292), ATG9B(291), POTEE(290), STK24(289), MAFK(288), TUBB4A(288), GSK3B(287), GATA2(287), GEM(286), SELENOK(285), AL603832.3(285), CTCFL(284), ZNF25(284), FDPS(283), PAOX(282), AP003419.1(282), CDK16(281), PKP2(280), ATP2A3(280), SQLE(277), TXN(277), DNALI1(276), PRPS1L1(276), SMIM35(276), PPM1M(275), AC011511.4(275), SLC7A10(273), HINT3(272), CLEC4F(272), TENM3(271), IGFBP1(268), DAAM2(266), PPID(266), ARRB1(265), KLF10(265), MRAS(264), MAOB(262), C3orf33(262), GPI(261), ACTR2(261), MAPK1IP1L(260), TMEM196(260), ERO1A(260), NANOS1(259), ELMO2(258), EXOSC6(258), DNAH8(258), EPHA7(258), FGF1(257), KRTAP21-1(256), SCGB1C2(256), NLRP2(255), CCL4L2(255), SETDB2(255), MIEF1(254), RIPK1(254), CAPS(253), FAM133A(253), PKN3(252), HSPA1L(252), AL691442.1(251), ENTPD1(251), RAET1G(250), SYK(250), RAB11FIP4(249), B4GALT4(248), RAD51(247), IAPP(247), C6orf223(246), HOXA7(246), EGLN1(245), PRKCB(245), LRIG1(244), OR10G3(244), CYP2F1(244), LGR4(244), PPP3CB(243), SYT8(243), ACTR8(243), GPR63(240), ALK(240), TMED1(239), CCR6(239), MERTK(239), TLNRD1(237), GOLGA6C(237), RCAN2(237), SMAD3(235), ZNF184(233), MPV17L(233), FRS3(232), C9orf64(232), UBQLN1(232), LY9(231), MTUS1(230), TPPP(230), ACLY(230), FAM72A(228), SYT10(227), ATP8B3(226), CDK5(226), GLI3(224), GLS2(224), GRAMD1B(221), TULP2(221), RB1(221), PCDHGA3(221), CDH7(220), TBXT(220), TENT5C(220), LRFN3(219), RHOB(219), RAD51D(218), DSG3(217), FLT3(215), TLR3(215), SGK3(214), MAP6(214), NPY(212), CSF1R(212), OCM(211), SLC26A4(210), B3GALT2(209), UGT2B28(208), AC008687.1(208), NOS1(208), SLC6A17(207), LRFN4(206), ZNF560(206), STRIT1(206), RAP1B(206), SPSB1(204), BCL2L13(203), SLC6A18(203), AL035460.1(203), ACSL3(203), AC010542.3(202), TCP1(200), ATG4A(199), F9(199), OCM(198), EGR1(198), SPX(197), CCDC13(197), VCY(197), GTF2B(196), MYBL1(195), FKBP9P1(194), CNTNAP3(193), MTHFD1(192), AC104581.2(192), WDFY2(192), PKP2(191), KIRREL3(190), ADIPOQ(190), COL4A6(188), TRPC6(187), PNPLA7(187), NEDD4(186), MFF(186), ATP6V1B2(186), NOXO1(185), KCNG1(185), GLI1(185), SORT1(184), AQP4-AS1(184), UBE2S(182), FOXO3(182), LINC01036(181), NME8(181), SEC14L2(181), TNNC2(181), RAET1E(181), SMIM15(180), AC244517.10(180), NME1-NME2(180), ARMT1(179), FRMPD2B(179), MAGEA9B(179), L3MBTL3(178), LIMK2(178), PPP2CA(177), RASL10A(176), C6(174), AC008763.2(174), RHOD(174), RGS20(173), WDR4(173), NUP50(172), REM1(172), RHEBL1(172), PPIA(172), FCRLB(171), PRKCB(171), KIF18A(171), TNFRSF11A(170), NGRN(170), CAMKK1(169), RIPK3(169), ZDHHC13(169), FCRLA(168), DMC1(168), TXLNB(166), CD79A(166), STK26(165), JAGN1(165), COL7A1(164), TREM1(164), TRIM7(164), SNAI3(164), ANP32B(163), CDC42EP5(162), PNMA8C(161), SPATA6(159), DDIT4(158), TRIM28(157), RB1(157), BCL2L2-PABPN1(157), SNAI2(156), ELAPOR1(156), HLA-DMB(155), CH25H(155), C5orf38(155), MT1HL1(154), SNTG2(153), HLA-DRB5(153), DAAM2(153), HJURP(152), CRYBA4(152), TFRC(151), RAET1L(150), FAM177B(150), HHIPL2(149), RUNX2(149), NPR1(149), XRCC5(148), RAP2C(148), MUC7(147), AC026464.1(147), CLCN1(147), FRMPD2(146), MCF2(145), GPR153(145), PTEN(145), SERBP1(144), SLC16A1(144), SLC10A2(143), TMX3(143), KLHL38(143), ZNF534(143), FBXO16(143), PITX1(141), LINC01036(141), NPIPA9(141), DUSP2(141), KRT83(140), NPY1R(140), CD177(139), TTC34(139), ACTG2(139), RBBP7(138), PRXL2C(138), AP000295.1(137), TMEM174(136), C12orf76(135), CXCL17(135), C1QL1(134), MTCL1(134), FAM74A4(134), EP300(134), SLC22A17(133), POLR3G(133), IFNLR1(133), GNAI1(133), GDPD2(133), CDH24(132), MFSD6(132), KSR2(132), AC010255.2(132), CCPG1(132), RHOU(132), GALM(131), ETV3L(131), POLR2C(131), ISL2(130), OR10G3(130), CNTNAP2(130), CALML5(130), ZCWPW2(130), VPS18(129), GPR31(129), CWC25(129), CTU1(128), ACTL10(128), IKZF3(127), TMEM52(127), C2orf80(127), CXCL17(127), NPIPA8(127), FGFR2(127), AQP8(127), ISG15(127), ZNF488(127), CUL4A(126), ZNF266(126), TMPRSS3(125), BEGAIN(125), CD4(125), AR(125), TMEM164(124), PCP2(124), MAP3K7(124), ANKEF1(123), CTSV(123), C16orf74(123), IGF1R(123), AIPL1(122), PPARG(122), CLPB(122), STRIP2(121), ST13P5(121), FOXP3(121), AL024498.2(120), MFHAS1(119), TEX9(119), EIF2AK3(119), CAMK1D(119), SLC52A1(117), MS4A1(117), SOWAHC(117), MGP(117), INSIG2(117), KLF4(117), AC004080.3(115), CHKA(115), VSX2(114), HK2(114), ANKRD40CL(114), EXO1(114), LRRC10B(114), EDAR(113), KRTAP2-3(113), PSMA4(113), CTU1(113), SLCO1B3(112), PDE6B(112), OLAH(112), PCP4L1(112), ADRA2B(112), PDE6B(112), CYP2A13(112), UBA52(112), KAT8(111), LCMT1(111), KDR(111), GART(111), ERO1A(111), MTOR(111), GMPR(110), GPHA2(110), KCNJ6(110), MYB(110), LONRF2(109), RALA(109), KIF19(109), TMX4(108), FIGLA(108), IRAK2(108), HS6ST1(107), PRIMPOL(107), HNRNPC(107), PRKG2(107), SNTB1(106), CCDC153(106), ANP32E(105), RHOBTB2(105), GNAI1(104), GRIN2A(104), GSTA3(103), EXT1(103), EIF2S3(103), ADIPOR2(102), GUCY2C(102), PNPLA3(102), SCD(101), CDKL2(101), ADGRD1(100), SHISAL2B(100), EIF2S3(99), PPP5C(99), PRRT3(98), RPP25(98), DMD(98), CLDN23(98), AC024592.3(98), KLF1(98), HSPA1A(98), CCER1(97), PCDHGC5(97), BLK(97), DUT(96), TM4SF20(95), SIGLECL1(95), PCDHAC1(95), UBE2S(95), PLPPR1(95), C19orf54(94), ARG2(94), EDAR(94), UBLCP1(93), TMED7-TICAM2(93), PADI6(93), POLR1C(93), EVX1(92), FAM71E1(92), AC104109.3(92), TSPY1(92), HS3ST2(91), SLC18A2(91), KLHL6(91), H2AC19(91), SNTG2(91), KLC3(90), MAP3K8(90), PTK7(90), CD200R1(90), GPR37(90), FBXO46(90), TMEM89(90), GSTM2(90), RHOBTB1(90), DDX24(90), IL17F(90), ALDOA(90), AP2A1(90), OIP5(89), PRKAR2A(89), SLC66A1L(89), PCDHA7(89), HSPA5(89), HDAC2(89), ZAN(88), FCRL1(88), KIAA2012(88), DIAPH3(88), LYPD5(87), GPX8(87), ADAMTS15(87), RWDD4(87), TRIM16(87), RND2(87), CCND1(87), OSCP1(86), PCDHB8(86), CD1E(86), SAAL1(86), PLK1(86), C8G(86), GOLGA8G(86), SRGAP1(86), VSTM5(86), AC005943.1(85), PCSK2(85), SALL1(84), ADGRF5(84), CENPM(84), CASC3(84), SERPINB7(84), GCSAML(84), ZNRF3(84), MLLT6(84), RAB7B(84), EEF1A2(84), FXR1(84), BDNF(84), ADH4(84), RFXAP(83), ZNF512(83), BMX(83), DIRAS2(83), WDR47(82), IRAG2(82), PLD4(82), AC073610.2(82), ZNF516-DT(82), PRKAG2(82), ENY2(82), TSPY2(82), ZNF280A(82), RMC1(81), ZNF394(81), OR2W5(80), GOLGA8S(80), DNM1(80), FAM9A(80), XRCC6(80), EVX1(79), LHX2(79), RNASE10(79), PCDHA13(79), ERCC1(79), PNPLA6(79), FOXN4(79), CXorf56(78), DMAC2(78), OTUD7A(78), ADGRG3(78), TCEAL3(78), BMP4(78), ARF3(78), RNASEL(78), GRIK2(78), RCAN2(78), AC097637.1(78), CALML5(77), HLA-DQA1(77), CYRIA(77), TUBA3C(77), PRB1(77), DOK1(76), SLC6A14(76), OR52E2(76), CRCT1(75), SLC6A2(75), CDSN(75), LYZL6(75), GPR1(74), DYRK1B(74), PRKAR1B(74), MAGEA9B(74), MDFI(73), CAPN13(73), PYGB(73), MGMT(73), ZKSCAN4(72), DNAJC1(72), FBN2(72), GGT6(72), LMNB2(72), SCPEP1(71), SLC22A23(71), MSX1(71), NCAM2(70), C10orf53(70), LRRC10B(70), RBMY1F(70), RDH16(69), SLAMF9(69), CAMK1D(69), ITGA6(69), FBXL21P(69), ACCSL(69), SALL1(68), ASCL2(68), PRSS3(68), RASD2(68), CA9(68), IL4(68), FAU(68), CDC25C(68), AC099811.2(68), ACRBP(67), DYRK4(67), RHOXF2(67), CPA5(66), PENK(66), FKBP3(65), ARMC12(65), AC073283.3(65), RHOBTB3(65), LPCAT2(64), CRHR2(64), MCTP2(64), KCNMB1(64), STARD4(64), ZCCHC4(64), BDKRB2(64), MANSC4(64), ELFN2(64), MS4A13(64), AK6(63), GYS1(63), FRMD8(63), DNAJC1(63), CPLX2(63), FAM189B(63), RNF180(63), SLC25A1(63), PHF1(63), TP53RK(63), SPATA13(63), PADI6(63), ZNF275(62), SNCAIP(62), CATSPERG(62), TRIM62(62), TMEM253(62), PHF5A(62), AQP4-AS1(62), FUCA2(61), ERCC1(61), CD99L2(61), MYL7(61), SSUH2(61), MLKL(61), MAL(61), VANGL1(61), CTAG1B(61), RBM8A(61), STK17B(61), ESR1(61), TTBK1(61), ASCL2(61), FNDC10(61), CBFA2T3(60), DCAF12L2(60), NEU1(60), COL28A1(60), CD9(60), NSUN7(60), CRISP3(59), CST8(59), IGF2BP3(59), TH(59), GPRIN2(59), KLC3(59), PIK3CA(59), DDX56(59), CPAMD8(59), KRT32(58), ST3GAL4(58), SLC2A4(58), AC004080.3(58), SPATS2(57), FAM104A(57), PPT2(57), TLE7(57), AHSA1(57), TSPOAP1(56), MT3(56), THYN1(56), C16orf54(56), RMDN2(56), SLC25A47(56), KLHL1(56), DNAJB4(56), HDAC3(56), UHRF1(56), EXPH5(55), TMEM143(55), CSMD3(55), MYO19(55), COL7A1(55), UBE2M(55), FAIM2(55), PKDCC(55), CTLA4(55), LRRC66(55), AMHR2(54), GTSE1(54), STEAP1B(54), KRT85(54), IL22RA1(54), COPG2(54), TCHHL1(54), PRB4(54), RTL5(54), UBE2Q2L(54), EIF3M(54), KCTD12(54), PAPLN(53), OR10H2(53), LINC00305(53), CTAGE15(53), RASD1(53), FAM219B(53), BTG2(52), HSD17B13(52), MAP3K19(52), NDUFA10(51), HSF2BP(51), C5orf64(51), ZNF879(51), CCR6(51), RASL11A(51), KDM6A(51), ZNF185(51), DMTN(51), CYB5R1(51), B3GALT1(51), RAP2B(51), RIPK2(50), IVD(50), LUZP2(50), AC092073.1(50), SQLE(50), RNF130(50), VWA3B(50), PPP2R2D(50), PRAC2(50), CDK3(50), ERLIN1(49), URM1(49), RIMS2(49), AHNAK2(49), JAK2(49), YY1(49), SMARCAL1(49), RPS6KA4(49), NBDY(49), CD40LG(48), KCTD15(48), UQCRB(48), CNBD1(48), C17orf107(48), MAPK6(48), PRDM2(48), MAPK15(48), LGALS17A(48), HMOX1(47), MRPS27(47), CASZ1(47), BTBD16(47), INTS7(47), KLHL8(47), MBIP(47), PCDHA4(47), FADS3(47), C1QTNF9(47), PNMA2(47), TRIB2(47), HSPA6(47), NDNF(47), NOTUM(47), PRRG1(46), LCA5(46), HSD17B13(46), FCRL6(46), ATP6V1E2(46), ZNF576(46), FAM83F(46), AC011452.1(46), CCDC28A(45), TMEM38A(45), CYREN(45), CHD1L(45), CENPU(45), AP1S3(45), NDST2(45), SLC22A12(45), TUBA3D(45), CDK6(45), NEDD9(45), CXCR4(45), CDKN1C(45), FAM83B(45), GPR35(45), CYP2F1(45), CLEC7A(44), LY6G5C(44), OR13A1(44), SNX29(44), TICRR(44), TENT5A(43), APOL2(43), TDRD1(43), ACO2(43), RBPJL(43), CD109(43), PRKACG(43), GAS2L1(43), SYT6(42), TMEM217(42), VPS37D(42), NPIPA5(42), SH2D5(42), CCDC28A-AS1(42), PRKACA(42), CREB1(42), P2RY13(42), CDH19(41), KPTN(41), NUPR1(41), TRIM27(41), LYRM9(41), SEMA3A(41), FLT1(41), NCL(41), WASHC2C(41), PPARA(41), COLCA1(41), HLA-DOA(41), KLF5(40), NGF(40), FAM156B(40), PCDHA12(40), FAM47E-STBD1(40), HTATIP2(40), CD5(40), SATB2(40), ATP8A2(40), SLF1(40), ZCCHC14(40), ECE2(40), PDE4B(40), FAM47E-STBD1(40), ZNF576(39), MNX1(39), CNPY1(39), PIP4P1(39), TAPT1(39), FOXL1(39), IZUMO1R(39), MFSD6L(39), AL136295.1(39), CISH(39), HMGN3(39), TUBAL3(39), SBK3(39), ENPP4(38), HAVCR1(38), GABRA2(38), PGS1(38), PCSK5(38), GRM6(38), CNNM1(38), ADCY9(38), KLHDC9(38), ALK(38), SMARCA1(37), PMS2P5(37), SWAP70(37), FAM110C(37), DCX(37), CDC5L(37), AL355916.3(37), AC073283.3(37), HAGH(36), TNFSF14(36), FRMD6(36), PRRT1(36), MAGEB1(36), TMEM233(36), AC004076.1(36), EPHA3(36), VPS18(36), ZDHHC2(36), YAP1(36), EPHA2(36), SLC27A4(36), MAP2K1(36), TENM3(36), AC069257.3(36), MSH4(35), NUCB2(35), B4GALT1(35), PIR(35), CCL20(35), PIK3CD(35), FADS6(35), UMODL1-AS1(35), PAX5(35), AC026954.2(35), HGF(35), EVX1(35), RET(35), EPHB3(35), RMDN2(34), HABP4(34), FGFBP1(34), MR1(34), MARVELD1(34), SETD3(34), SHISA4(34), EEF1G(34), HRH3(34), RERGL(34), RNASE1(34), REEP2(34), HEY2(34), C7orf69(34), SFTPB(34), LRRK2(34), PSMC6(33), RAB29(33), CPA2(33), LDHD(33), SEPTIN1(33), LINC00477(33), GAB2(33), MFSD12(33), LRRTM1(33), ADAD1(33), FADS6(33), C3orf85(33), BORCS8(33), ZMYND12(32), DESI1(32), NMI(32), CCDC51(32), TMEM64(32), MEIKIN(32), HMMR(32), SGK1(32), GPAM(32), DCLK1(32), NKX2-1(32), PAOX(32), PPID(32), CHEK2(32), SHISA4(32), PDE10A(31), ONECUT2(31), C10orf95(31), FLRT1(31), UBAC2(31), ZNF787(31), FARS2(31), ADAMTS3(31), RIMBP3C(31), H2AX(31), ZSCAN16(31), CAMKK1(31), PVR(31), WDR91(31), MISP3(31), RIT1(31), TMEM233(31), NCOA4(31), ELP4(30), C9orf40(30), LUM(30), GPATCH11(30), IRX6(30), FSIP2(30), AP000781.2(30), OCM2(30), RNF180(30), TGIF1(30), TMEM125(30), KCNE1(30), SERPINB5(30), TDRD15(30), SSX2B(30), ZNF330(29), COX16(29), CHAD(29), PLPPR1(29), ZMAT1(29), FAM83B(29), CLECL1(29), BRINP2(29), C4orf48(29), LMAN1(29), ERO1B(29), TBX18(29), IL6(29), ZNF497(29), ZNF555(29), C1orf210(29), TAB1(28), CNIH1(28), ATP8A2(28), SPATA18(28), TERF2IP(28), PXDC1(28), PKIA(28), RPE(28), KRTAP3-1(28), PITX1(28), DROSHA(28), FLG(28), SLC34A2(28), PLCG2(28), FAM221B(28), AP000781.2(28), TRIM29(27), LIPT1(27), F2RL1(27), PLK3(27), FMR1NB(27), SLC24A3(27), LACTBL1(27), ANKRD34A(27), CHD1L(27), RERG(27), SLC4A5(27), SOWAHC(27), RTL5(27), ATL2(26), EDA2R(26), BIVM(26), TLR2(26), ASCL4(26), PAPSS2(26), LINC01138(26), UBE2D1(26), BMP5(26), SUMO1(26), RSPO3(26), LDLRAD2(26), KLRG2(26), EXOSC6(26), AL117348.2(26), TBC1D3H(26), C7orf77(26), ASB4(25), DEPDC1B(25), MGAT4A(25), ERO1B(25), NLRP1(25), CDADC1(25), DBP(25), CCDC34(25), AMHR2(25), NIPA1(25), LRRC63(25), GAS2L1(25), EED(25), GPC4(25), MTHFD1(25), CCL20(25), PRKAG3(25), TRIM24(25), LRRC8A(25), ZIC3(25), TMEM196(25), FAM156B(25), TCHHL1(25), PGAM4(25), H4C9(25), DNAJA1(24), EBF3(24), BCAS4(24), RBM42(24), ARSG(24), ADPRHL1(24), MAGEA8(24), FAM122C(24), BSDC1(24), TTC16(24), NDNF(24), NPIPA1(24), SBK3(24), PRKAR2B(24), CCT8L1P(24), FGFR3(24), SLC26A4(24), IGF2BP3(24), USP6NL(24), NAA11(24), UTY(24), MFSD6L(24), FAM243B(24), BMP7(23), HPX(23), DHDDS(23), MMP27(23), FAHD2B(23), KCNF1(23), TM4SF4(23), CDKN2AIPNL(23), WDR3(23), STAG3(23), ATP2B3(23), SRI(23), GGA2(23), RHPN2(23), CPLANE2(23), SYT6(23), RAB40B(23), AMT(23), PROSER2(23), TNIK(23), MS4A1(23), MMADHC(23), EMX2(23), CNBD1(23), CD8B2(23), USP27X(23), KCNH2(22), TCL1A(22), CDC42EP3(22), MAP2K1(22), MBOAT1(22), IL1RAPL2(22), PCDHGB1(22), MSH4(22), TRPA1(22), MAPK8(22), PRLR(22), TTR(22), RCBTB1(22), AZIN2(22), LYAR(22), RAET1L(22), IRX3(22), WFDC10B(22), NELL2(22), TEKT4P2(22), AC099489.1(22), AC073612.1(22), SCGB1C2(22), DCN(21), BIRC3(21), CHRNE(21), LANCL1(21), ZSCAN1(21), IQCC(21), SCGB3A1(21), KRT6C(21), ATP11AUN(21), MTRNR2L1(21), ENSG00000277669(21), MAP3K20(21), GRB10(21), PPP3CB(21), CDK18(21), MTFR1L(21), ATL2(21), LRFN3(21), GMPR(21), TTC12(21), GNA14(21), TREML1(21), STEAP1(21), LEP(21), PDIK1L(21), ACTL9(21), FSIP2(21), ADH1C(21), SMIM32(21), RAB27B(20), SULT2B1(20), TIMMDC1(20), PIP(20), SYTL3(20), IHO1(20), CD164L2(20), C14orf39(20), MYCBP(20), HLA-DQA2(20), TBC1D3E(20), CCDC28A(20), ZNF302(20), FAAH(20), EGLN3(20), TCEAL4(20), GPR55(20), RALB(20), ADCY1(20), STAT3(20), COL22A1(20), VANGL1(20), TAS1R2(20), NWD1(20), TEX45(20), LPAL2(20), AL132780.3(20), TBC1D3D(20), SH3YL1(19), ISOC1(19), PPP1R13L(19), WDR91(19), CKAP4(19), SPATA17(19), TGIF1(19), C9orf135(19), RTL1(19), IGF1(19), ANAPC4(19), GGT1(19), CD99L2(19), CNTN3(19), RAP2A(19), RASL11B(19), NTS(19), PIWIL4(19), MPP7(19), SP8(19), TAGAP(19), DDX23(19), GRB2(19), TTLL12(18), CTSZ(18), ATG10(18), MICU3(18), RUNX1(18), CCDC85B(18), LDLRAD2(18), C19orf67(18), FAM47E(18), ASB13(18), ZSCAN5B(18), CDC42BPB(18), SYCE3(18), XK(18), SLC13A1(18), KCNK16(18), MADCAM1(18), AMPD1(18), SLC7A10(18), ACTR1A(18), SHF(18), HSPD1(18), TRMT10A(18), ITGB1(18), RNASEK-C17orf49(18), PRRT3(18), TBXT(18), FAM98B(18), MIR1-1HG-AS1(18), CDK5R1(18), LRRC3B(18), KLHL32(18), PRELP(18), MZT1(18), TMEM231(18), MEIKIN(18), GSTA2(18), LINC02218(18), HOXB7(18), CCDC187(18), GOLGA8T(18), STRAP(17), JAG1(17), VIPR2(17), SCAF1(17), ANO1(17), PLEKHS1(17), FZD1(17), ZNF569(17), EOLA1(17), TMX2(17), OPN3(17), CDK14(17), TOP2B(17), SLC5A5(17), PCDHB6(17), TNFSF14(17), IRF4(17), MBIP(17), PDE7B(17), MYPOP(17), ZNF682(17), CT83(17), LY6G5C(17), TEX13A(17), CWC25(17), FAM27E3(17), RCC1L(17), MLLT6(17), AC117457.1(17), FKBP5(16), DUSP3(16), CRISP2(16), PGPEP1(16), NLRP4(16), SENP8(16), CDH2(16), HPSE(16), FOSL1(16), MRFAP1(16), HMSD(16), AC055811.2(16), AC008758.5(16), RPS6KA6(16), PSMC6(16), HNF4A(16), NCALD(16), SORL1(16), KLK3(16), OLAH(16), SLC18A2(16), PGAM1(16), RRM2(16), ZNF77(16), C14orf39(16), EOLA1(16), LBH(16), SMIM35(16), RAB7B(16), PVR(15), PF4V1(15), IL17A(15), PARD3B(15), CEP104(15), COQ8B(15), GPR55(15), CCN3(15), GLB1L2(15), SLC6A1(15), TMEM41A(15), SLC9B2(15), SYAP1(15), TM4SF1(15), GPR37L1(15), METTL7A(15), PRB3(15), APCDD1L(15), ZNF888(15), HSBP1L1(15), SYS1-DBNDD2(15), TUBB8(15), ENTPD2(15), ROGDI(15), DPYSL2(15), RAB14(15), WNT1(15), STATH(15), CBFA2T3(15), RCBTB2(15), MAP2K5(15), DIRAS3(15), CCDC182(15), SEPTIN1(15), RGPD6(15), PRB3(15), CALM1(15), LINC02693(15), RHBDD2(14), ENTPD2(14), SLC44A1(14), WDR62(14), GPC4(14), KMT5B(14), RIPOR2(14), PLBD1(14), TMEM178A(14), GPR15(14), TIMP4(14), HSD11B1L(14), KNDC1(14), PRSS38(14), PAGE2B(14), ABCC8(14), RAB27B(14), WFDC2(14), RBBP7(14), PPP2R1A(14), ANXA10(14), CCT4(14), CRISP2(14), IVD(14), KSR1(14), RHBDL3(14), HUNK(14), GALM(14), FARS2(14), IFNA5(14), SLC6A1(14), BEND5(14), YWHAB(14), LRRC63(14), FOSL1(14), PLEC(14), ADGRA1(14), ATP11AUN(14), KLRC2(14), ZNF254(14), CD302(14), KIR2DP1(14), TESK2(13), ZFR2(13), FCRL2(13), TMEM155(13), SERPINB12(13), AVEN(13), TEX44(13), RFLNA(13), SEMA4B(13), COL4A5(13), CD302(13), SYNJ2BP-COX16(13), AC018755.2(13), CLUL1(13), NOD1(13), PTPN6(13), SET(13), GNMT(13), SCAF1(13), MLIP(13), SNX30(13), HACD1(13), PKD1L2(13), ZNF16(13), PRR15(13), LINC00518(13), CEACAM19(13), H2AX(13), LINC00336(13), H2BC12(13), ALG3(13), AL136295.1(13), PRKCH(12), PLEKHH1(12), GUCY2F(12), ZSWIM3(12), PI4K2A(12), MRPL10(12), PIGX(12), FAM178B(12), TMEM50A(12), ST6GALNAC3(12), SERINC4(12), DPPA3(12), FBXL22(12), LINC02693(12), SYT3(12), SPATS1(12), COPZ2(12), NLRP2(12), DKK3(12), SDCCAG8(12), ELAVL1(12), MAOB(12), PSEN1(12), CDC14B(12), ASAP3(12), CD40LG(12), MYH1(12), DUSP22(12), FGF1(12), DHDDS(12), RFTN1(12), LEF1(12), SYT14(12), IGSF1(12), LYPD5(12), FGFR4(12), TMEM41A(12), FBP1(12), TMEM63C(12), SLC25A33(12), CDY1(12), RND1(12), TNKS(12), TLR10(12), ZNF843(12), RFLNA(12), OR51B4(12), LDB1(12), INPP5B(12), CYP1B1-AS1(12), AMACR(12), ZNF512(12), AC006486.1(12), SLAIN2(11), SLITRK3(11), GNMT(11), PSPN(11), FBXO44(11), MBD1(11), CTF1(11), ESYT3(11), DPY19L1(11), PHLDA3(11), CCDC60(11), CCDC190(11), KLHL32(11), SLC29A3(11), NT5C1B-RDH14(11), SSX4B(11), SARM1(11), DNAH5(11), EIF2B3(11), MAGT1(11), FCER2(11), P2RX1(11), HPX(11), FNDC4(11), UBA2(11), CRB1(11), KIAA0319(11), MEAK7(11), ARRB2(11), MFHAS1(11), STC1(11), SNX7(11), RHO(11), SAAL1(11), DCAKD(11), CTBP2(11), GRAMD2A(11), OTOP2(11), FAM111B(11), ADH7(11), OXCT2(11), RPL36A-HNRNPH2(11), AL136295.3(11), ANKRD34A(11), MYO19(11), ZNF821(10), EHHADH(10), LMAN2L(10), PMEPA1(10), RHPN2(10), DUSP10(10), TRIM55(10), SPC25(10), CENPH(10), SFXN1(10), SRR(10), KLHL25(10), C5orf52(10), ASB12(10), DEPDC1B(10), GPC1(10), SPEG(10), ST6GAL1(10), RABL2B(10), HDAC6(10), TTC28(10), SALL1(10), RHEB(10), EIF4H(10), CAND1(10), TXNDC15(10), SPATS2(10), APOE(10), PHF11(10), DERL1(10), CCN3(10), MCL1(10), ARHGAP18(10), ADHFE1(10), REXO4(10), ADCY8(10), GPX8(10), RIC3(10), MS4A14(10), CEL(10), RELA(10), LRRC75A(10), ODF3L1(10), UMODL1-AS1(10), GPR141(10), FAM217B(10), ZNF492(10), PAGE2B(10), CTAGE8(10), CLDN23(10), AL049634.2(10), AC008763.2(10), DDX52(10), DEF6(9), FSTL3(9), ABCD1(9), IL27RA(9), LHPP(9), FBXO9(9), IRF6(9), PCDHB14(9), THAP10(9), CLIC6(9), NIBAN3(9), CANT1(9), FJX1(9), TEX33(9), C17orf58(9), IDO2(9), ARMH1(9), AP000721.1(9), CASP10(9), CUL1(9), PRKCZ(9), ATP5F1D(9), FZD3(9), LHX2(9), SOD3(9), SAYSD1(9), GBE1(9), PRAMEF2(9), NKX2-4(9), FAM104A(9), ACTL6A(9), GREB1L(9), EFHD2(9), CYP4B1(9), SNCA(9), ZAN(9), TKFC(9), LYZL4(9), IKZF3(9), PITX2(9), LINC01600(9), SERPINB7(9), DRD5(9), CST5(9), RBKS(9), ZNF570(9), NLRP13(9), PRM3(9), HNRNPCL4(9), ZNF93(9), NANOS3(9), LITAF(9), ARMCX6(9), C9orf92(9), ZNF888(9), VSTM5(9), LINGO3(9), PPP3R1(9), ARIH2OS(9), TSPY3(9), ZNF737(9), PEDS1(9), SYNJ2BP-COX16(9), AC018755.2(9), CT45A10(9), LENG9(9), H4C7(9), NKAIN1(8), MROH8(8), CISD1(8), WFIKKN1(8), CBWD2(8), HORMAD1(8), THSD7B(8), RPIA(8), PPP2R2B(8), TMEM63C(8), MS4A14(8), TACR3(8), TOMM5(8), NHEJ1(8), COL13A1(8), KRTAP10-3(8), LINC00205(8), KIR3DL3(8), GBA3(8), CCDC166(8), LENG9(8), CX3CL1(8), ZNF275(8), HAL(8), CDKN3(8), CTSZ(8), MROH8(8), EEA1(8), PDGFRB(8), YPEL5(8), C10orf95(8), THAP10(8), THEMIS2(8), IER3(8), KYAT3(8), LPAR6(8), ZNF287(8), HORMAD1(8), MYH15(8), ARMT1(8), LRRC27(8), CNBD2(8), PFKM(8), OBSCN(8), NEUROD1(8), SNIP1(8), CCDC51(8), UCMA(8), HDGFL3(8), ZNF3(8), NLRC3(8), CXXC4(8), GCSAML(8), SOCS5(8), MYEOV(8), TRIB1(8), TCP11L1(8), C5orf64(8), HLA-DQB1(8), TMEM86B(8), SIAH2(8), PRKAG1(8), RNASE10(8), LRRC37B(8), KRT14(8), COL4A5(8), DTHD1(8), ARHGAP11A(8), CXorf66(8), LINC00326(8), SAA2-SAA4(8), GPR142(8), DMRTC1(8), TAF15(8), KCNE1B(8), SPATA31A5(8), COCH(7), LIF(7), NUDT15(7), APCDD1(7), TGM4(7), SPRY1(7), SCNN1B(7), SLC25A42(7), LDOC1(7), EPGN(7), MZT1(7), SMIM7(7), HNRNPUL2-BSCL2(7), MRPS17(7), SMIM11B(7), KCNE1B(7), ARNTL2(7), PKN2(7), FOSL2(7), PAK3(7), SMARCA2(7), NDC80(7), SERPIND1(7), PVALB(7), SCML2(7), CHCHD2(7), MYF5(7), SLCO1B3(7), KHDRBS2(7), EPB41L5(7), POMC(7), EHBP1(7), VPS4B(7), PCDHB8(7), LRRC29(7), IL1B(7), FRMD8(7), DLGAP5(7), RIPK3(7), EXOSC2(7), DLG4(7), FAM189A2(7), BTBD16(7), SUOX(7), DYRK3(7), CSGALNACT1(7), SYT8(7), AMN1(7), ARL11(7), PLOD2(7), MR1(7), ZFYVE27(7), GAB3(7), ZNF394(7), KCNF1(7), F2RL1(7), STK32C(7), MOGAT2(7), XRRA1(7), DTYMK(7), ZBTB49(7), AGXT(7), DAB1(7), GOLGA8Q(7), EXT1(7), DNM1P46(7), DDX41(7), TMEM50A(7), CCR4(7), ADAP2(7), TAFA3(7), HYAL3(7), TSPYL4(7), C5orf52(7), PLSCR1(7), NCCRP1(7), VN1R5(7), AL139353.1(7), C6orf47(7), CD177(7), NUDT19(7), PPT2(7), TSPAN19(7), TRHDE-AS1(7), DNAAF4(7), AC068896.1(7), C19orf84(7), MTRNR2L12(7), KRTAP10-7(7), FAM25BP(7), ZIC2(6), ASB1(6), CAPN6(6), MID2(6), GCKR(6), TMPRSS11E(6), APOL1(6), SLC25A17(6), SGPP1(6), GFAP(6), IL10(6), UGT3A1(6), SESN3(6), KLHL35(6), FYCO1(6), PTK2(6), PCDH7(6), HNRNPA0(6), PGPEP1L(6), TANGO2(6), CLDN24(6), HYKK(6), ASTL(6), ZNF140(6), MUC21(6), ARRDC5(6), TMEM213(6), FMO9P(6), AC010327.2(6), TBC1D3I(6), MBTPS2(6), SNAI2(6), SARS1(6), MSMO1(6), LY75(6), CYFIP2(6), ATP2B4(6), DNAJC25(6), GNA15(6), HIPK2(6), CASS4(6), SEL1L3(6), NLRP1(6), HNRNPM(6), FGF14(6), NBN(6), STK3(6), STEAP1B(6), GPLD1(6), EVA1A(6), HOXB5(6), P4HA1(6), RAB9B(6), MBOAT7(6), EIF2S2(6), SGPP1(6), YEATS4(6), FBXL16(6), WDFY4(6), HABP4(6), NAPSA(6), EIF2S1(6), TESPA1(6), ZSCAN9(6), FCHSD2(6), SQOR(6), CYP1B1(6), SLC38A4(6), PDX1(6), RMC1(6), ZMYND15(6), DTL(6), ARF1(6), ITPKB(6), CCNB3(6), LRP12(6), POLR3A(6), HMGA2(6), AK9(6), MYO1E(6), CD1D(6), GPBP1L1(6), COX6B2(6), TEDC2(6), NUDT2(6), PHYHIPL(6), VDAC2(6), NDST2(6), GPRIN1(6), ADRA1B(6), CMTM8(6), KSR2(6), LPAR3(6), PARP15(6), AGFG1(6), NWD2(6), GSTA3(6), SLC16A11(6), SPHK1(6), SGF29(6), RPS6KA3(6), ERN1(6), CSRNP3(6), OFCC1(6), FAM43B(6), ANKRD45(6), TMPRSS2(6), SPEM2(6), TEX33(6), SPATA21(6), IDO2(6), RNF222(6), SLC29A3(6), PEG3(6), TMEM239(6), HLA-DRA(6), GPX3(6), KRTAP4-9(6), ZNF879(6), ZNF702P(6), ZFP91-CNTF(6), AC104581.2(6), AC104109.3(6), CCL15-CCL14(6), BARX2(5), LY75(5), ZCWPW1(5), SERPIND1(5), MOSPD1(5), MOGAT3(5), CHRNB4(5), SH2D3A(5), SOX3(5), KIAA0513(5), FCHSD2(5), BCAR3(5), FBLN7(5), LRRC27(5), GLB1L3(5), RIC3(5), SPATA33(5), FBXW10(5), KLHDC7A(5), OXTR(5), TSPYL4(5), ZNF669(5), NUDT19(5), AC002310.4(5), GAS7(5), SCN4A(5), CYB561(5), CLTCL1(5), FSTL3(5), MBD3(5), DNAJC10(5), MOK(5), XPO1(5), PLOD1(5), LPCAT2(5), IKZF5(5), PNPLA3(5), PPP2CB(5), GYS1(5), VRK3(5), DBP(5), IL17A(5), CAP2(5), KIF20A(5), PFDN1(5), IRF6(5), MUC5B(5), ATP8A1(5), BTN2A3P(5), SSUH2(5), PTPRE(5), NUMB(5), TBRG4(5), HS6ST1(5), ANKRD42(5), NKD1(5), IRF8(5), ERBB2(5), CYP17A1(5), GPHA2(5), TMEM86A(5), CWC27(5), ENPP3(5), MAGEA8(5), WDR19(5), PDE9A(5), FAM189B(5), CD200R1(5), CPA3(5), CREBRF(5), C8orf34(5), MRPL16(5), MARS1(5), SCNN1B(5), TMEM150A(5), TACR3(5), HOXD4(5), KRT8(5), CHCHD7(5), FOXB1(5), CES4A(5), PHLDA3(5), SPRYD4(5), C20orf197(5), HNRNPCL1(5), HTR1D(5), C11orf71(5), TMIE(5), TMEM252(5), GET1(5), PRR30(5), CHCHD2P9(5), ERAS(5), C19orf67(5), ZNF626(5), C19orf54(5), SUMO2(5), PAX5(5), ILRUN(5), ZNF429(5), RPE(5), SH3BGRL2(5), TMEM184B(5), NEU1(5), PRAMEF9(5), TMEM170B(5), MFSD2B(5), SIAH3(5), ZNF880(5), EXOC3-AS1(5), ZNF630(5), FAM30A(5), C2orf92(5), LEFTY1(5), GPR162(5), OR11H7(5), GOLGA8S(5), AC090227.2(5), AC090360.1(5), MAGIX(5), DOC2B(5), MPC1(4), ST6GALNAC2(4), CA12(4), MRPS31(4), ZNF451(4), ST3GAL5(4), DDX59(4), FYTTD1(4), CD70(4), PROZ(4), TPST2(4), KCTD1(4), PADI3(4), ZNF214(4), MEPE(4), TSPAN7(4), TBC1D31(4), TSC22D3(4), MPZ(4), CCDC116(4), ASRGL1(4), CCDC68(4), SOX14(4), SPRR1B(4), PNMA8A(4), EFHC2(4), BLOC1S5(4), ZNF79(4), NUP62CL(4), SH3BGRL2(4), ALPK2(4), EXOC3-AS1(4), FBXO17(4), ENSG00000183729(4), GCLC(4), DDX11(4), BARX2(4), WDR37(4), KCNH2(4), STYK1(4), CTSA(4), ZC3H15(4), MGAT4A(4), ZNF506(4), CAD(4), POMGNT1(4), MYL12A(4), FA2H(4), CTSH(4), ANXA13(4), AURKC(4), CRHR2(4), ELF2(4), CYTIP(4), ST3GAL5(4), ATF2(4), LRRC42(4), IRAG2(4), CYP20A1(4), ONECUT2(4), GPR75(4), PLBD1(4), GAD1(4), AIPL1(4), F12(4), TIMM10B(4), PCNA(4), PDE6A(4), NGF(4), PDGFRA(4), RIPK1(4), TTPA(4), NXPE4(4), REM2(4), RLBP1(4), ABCC12(4), WDTC1(4), CNGA3(4), NICN1(4), KCNMB1(4), HDAC8(4), SIDT2(4), HNMT(4), FOXO1(4), GPATCH11(4), EPG5(4), ELMO1(4), SLA(4), DDX19B(4), GIP(4), HIPK4(4), MPP3(4), PPM1K(4), GUCY1A1(4), SHH(4), VCP(4), MFAP4(4), HSP90B1(4), LDHC(4), RBPJ(4), PKIG(4), TSNARE1(4), SPSB1(4), CLEC7A(4), IL16(4), FBXO45(4), FOXG1(4), RPP38-DT(4), TAC4(4), YIPF7(4), ERICH3(4), ALX1(4), OR56A4(4), PGPEP1L(4), USP18(4), BRI3BP(4), INPP5J(4), METTL7A(4), ROR1(4), SP1(4), FAM9C(4), C6orf132(4), C10orf99(4), S100A16(4), ZFP28(4), ZNF43(4), KCNRG(4), LRRTM3(4), APCDD1L(4), SREBF2(4), LINC02868(4), PCDHA7(4), INSYN1(4), SYT3(4), GNAT3(4), SPINK13(4), C1orf229(4), C5orf67(4), HNRNPUL2-BSCL2(4), MIF(4), TMEM150C(4), FOXD1(4), AL512785.2(4), CCDC166(4), AC107871.1(4), KIR3DP1(4), BAHCC1(4), CYFIP1(4), CCL4L2(4), NEFL(4), PPIAL4F(4), CLCA1(3), DGCR2(3), SNW1(3), SLC25A14(3), SLC22A2(3), FBXO2(3), EEF1AKMT3(3), KCNS1(3), NT5E(3), MARCHF9(3), SYT2(3), SSC4D(3), PRDM14(3), TMEM163(3), FUT6(3), WDR19(3), CD1B(3), FMNL3(3), FCAMR(3), LMBRD1(3), FBXO45(3), ZDHHC24(3), CHST2(3), HOXD8(3), POU6F1(3), ZSWIM9(3), SAMD9(3), AP002373.1(3), AP002748.5(3), GLRX2(3), MYO16(3), RRM2B(3), ELN(3), ITIH4(3), INTS13(3), SNCAIP(3), PKM(3), RPS6KA2(3), WDR62(3), FMO4(3), OPHN1(3), PTPRC(3), KCNK2(3), PPIE(3), ALG9(3), RTRAF(3), SULT2B1(3), RAPGEF4(3), AGO1(3), NANS(3), HCN2(3), CRKL(3), GRK3(3), DESI1(3), CNIH1(3), CD40(3), HCK(3), ZNF516(3), SLC25A14(3), KLHL4(3), CCL22(3), EIF3J(3), UBE2W(3), FCGRT(3), CCNE1(3), SYNGR4(3), ERF(3), RPL28(3), RAD51C(3), PTGES3(3), KRT18(3), ACRBP(3), GNB3(3), PHC1(3), KLRB1(3), VNN1(3), SLC29A1(3), TENT5A(3), THG1L(3), GOLPH3(3), NR3C1(3), TIMMDC1(3), PRKAR2A(3), GADD45A(3), BCAS2(3), SDHB(3), DYNC2I2(3), YIPF4(3), GPR31(3), NAA50(3), ZC3H7A(3), NMI(3), KCNS1(3), FASTKD3(3), COL21A1(3), TRIP10(3), RBM42(3), SIN3B(3), RAC2(3), NEDD8(3), PGPEP1(3), PNCK(3), EDA2R(3), CASP9(3), FST(3), KLRC1(3), YARS1(3), CYP27A1(3), PCDH8(3), ITM2B(3), IL10(3), CDK5RAP2(3), TLR4(3), TMEM8B(3), IGFBPL1(3), ETFBKMT(3), MARCHF9(3), DUSP6(3), MCTP2(3), CIB3(3), SAE1(3), FAM71E1(3), PRDM16(3), PTPRF(3), LHX9(3), THSD7B(3), AC073896.1(3), ILDR1(3), SHISAL2B(3), PSPH(3), RSU1(3), SAA4(3), ZNF214(3), C2orf50(3), THRSP(3), C4orf33(3), FRMD4A(3), VENTX(3), TMEM123(3), C16orf89(3), RAB39B(3), GPR61(3), DHRS1(3), IFNAR2(3), HOXB13(3), CLIC6(3), NLRP4(3), FMNL3(3), AKNAD1(3), CRYGC(3), ELOVL7(3), CRYL1(3), ANKRD2(3), CFAP52(3), CHP2(3), GNGT2(3), MYO5B(3), ZNF526(3), TXNDC2(3), LETM1(3), PXDC1(3), VXN(3), OTUD7A(3), UBE2E3(3), NCBP2L(3), HSFX1(3), MALT1(3), GNG12(3), HPSE(3), TNFRSF10C(3), CRYBG2(3), B3GNT8(3), NIM1K(3), DMAP1(3), CIITA(3), MB21D2(3), SHISA2(3), CLRN3(3), EHMT1(3), ZNF322(3), MRPS11(3), CCDC125(3), ZNRF3(3), FAM110C(3), DMRTC1B(3), CCDC137(3), CLDN24(3), KIF18B(3), SECISBP2(3), MAGEB5(3), MRTFA(3), TLR7(3), CD47(3), ACSL5(3), WWP2(3), RCSD1(3), CAPZA2(3), RIPPLY2(3), ASAH2B(3), OR2H1(3), C9orf135(3), FBXO48(3), KRTAP9-6(3), SMIM7(3), ADM5(3), ELFN1(3), SRRM5(3), MRLN(3), CFAP97D1(3), TEX35(3), ZNF722P(3), PCDHAC1(3), OR13A1(3), ZNF865(3), SRSF8(3), RASSF5(3), PTGES3L(3), AC010327.2(3), AC024592.3(3), SLC6A14(3), SMIM17(3), ATP6V1FNB(3), ADRA2B(3), FCGBP(3), OR4E1(3), ZNF229(3), C11orf98(3), CASS4(2), GSTT2(2), SLC52A3(2), PLIN3(2), ETHE1(2), PRUNE2(2), TMEM97(2), STEAP3(2), PLXDC2(2), KRT17(2), PRPH(2), MRPL44(2), MED4(2), GH2(2), STRA6(2), ANP32D(2), HNRNPLL(2), HTR3B(2), SETD9(2), SIM2(2), KIAA1586(2), DEGS2(2), C1QTNF4(2), GPR156(2), LYNX1(2), KCNJ14(2), CCDC157(2), ZNF257(2), ZNF98(2), GPATCH3(2), PCDHGA1(2), KBTBD13(2), PCDHA11(2), AL513165.2(2), ST20-MTHFS(2), AC105052.3(2), TMEM176A(2), KLHL13(2), NDUFAF7(2), PDK2(2), DNAH9(2), VTA1(2), ZBTB32(2), NR1H4(2), TBPL1(2), ASTE1(2), VCL(2), FBXO42(2), MAPK9(2), KIF1B(2), CDK17(2), HAGH(2), ERBB3(2), TLE2(2), ASB1(2), COASY(2), EPHA8(2), MYO3B(2), P2RY10(2), NKAIN1(2), HADHA(2), ABCB1(2), AQP6(2), MMP2(2), ARHGAP4(2), RGS1(2), PLEKHG2(2), CDC23(2), TMEM38B(2), HSD17B7P2(2), SYNGR1(2), RANGAP1(2), ASB2(2), SLC52A3(2), DNTTIP1(2), GPR143(2), MOSPD1(2), MCF2(2), DHRS12(2), ZNF821(2), CSK(2), SPAG1(2), CLPTM1(2), CRX(2), SERPINE1(2), TMEM176B(2), TNFSF8(2), UBE2R2(2), HPS1(2), RPS6KB1(2), IL2(2), BST1(2), PRR4(2), COPZ1(2), HCFC2(2), ZNF451(2), SRF(2), GABRG2(2), PDE4D(2), LIFR(2), SLC30A3(2), CLIP4(2), FANCL(2), IL1R2(2), ID2(2), EPHA4(2), ZNF684(2), PIK3R3(2), RCAN3(2), INVS(2), DLST(2), ZC2HC1C(2), ARMH3(2), TEK(2), CCDC170(2), NUDCD1(2), HSPH1(2), ZFP30(2), APAF1(2), ABCC11(2), UBL3(2), LPGAT1(2), G0S2(2), PMS2P5(2), INHA(2), CTCFL(2), PI3(2), TBCC(2), CDKN1A(2), ID1(2), PRR12(2), LRRC61(2), KRT17(2), CLN6(2), BBOX1(2), CDC16(2), ZBTB46(2), CEP85(2), SLC6A8(2), SYNE1(2), GFAP(2), BARX1(2), PDHA1(2), SERPINF1(2), ANKEF1(2), PCED1A(2), SEC14L4(2), TMTC1(2), GSTM1(2), CYP2J2(2), ELF5(2), COQ10A(2), KIAA1614(2), MED4(2), IL36A(2), SLC22A7(2), FGFBP1(2), MGARP(2), ANXA7(2), RASGEF1B(2), INTS12(2), MTMR6(2), GRTP1(2), BBS4(2), SEC11A(2), TIGD7(2), SPATA22(2), C18orf21(2), SLC16A3(2), TBCD(2), TNFRSF11A(2), APP(2), ZNF787(2), NOSIP(2), CFAP74(2), MAEL(2), SYT2(2), NPHP1(2), FBLN7(2), GALNT13(2), NYAP2(2), CPNE9(2), ATG12(2), GFRA3(2), SLC18B1(2), SSC4D(2), FATE1(2), PAMR1(2), CTF1(2), DCP1B(2), ITIH2(2), PABPC3(2), TMEM163(2), TMEM178A(2), SPOCK1(2), CDYL(2), RANBP2(2), PTPRR(2), CMIP(2), KCTD15(2), GDPD1(2), ASZ1(2), PLCL2(2), CYP2U1(2), MARVELD1(2), CLDN8(2), MPZ(2), ATP5MC1(2), ZDHHC1(2), ZBTB8A(2), FTCD(2), YDJC(2), SHANK2(2), FGF19(2), EXTL2(2), CFAP221(2), TDRD10(2), CCT3(2), ADORA1(2), GLB1L(2), NFASC(2), COX18(2), POLR2H(2), H2AZ1(2), ZNF589(2), WDR41(2), CDC20B(2), GJB7(2), AK8(2), GLB1L3(2), AMN(2), ASPG(2), ACSM1(2), GLYATL1(2), NOD2(2), SNX20(2), HSD11B1L(2), KLK13(2), LDLRAD4(2), ADAL(2), PARM1(2), RNASE6(2), CXCL8(2), FASN(2), GPR37L1(2), LGALS9B(2), ELOVL6(2), DLGAP1(2), CAVIN3(2), ZNF581(2), ZIK1(2), GPR34(2), FAM90A1(2), SHLD1(2), DHCR7(2), PLK3(2), SLC16A13(2), UCP2(2), GAPT(2), HOXD8(2), AMIGO3(2), ZNF135(2), FOXL1(2), TYMSOS(2), RIMKLA(2), OR2B11(2), SPINK6(2), ERBB4(2), KLHDC7A(2), RAD23A(2), ZNF154(2), MFSD5(2), NPIPA1(2), SETD3(2), TANGO2(2), PNMA3(2), CTAG1B(2), PPP1R2(2), POU6F1(2), GDF3(2), EFNA5(2), ODF4(2), ZSWIM9(2), LINC00839(2), WWOX(2), FCAR(2), ZNF501(2), NAP1L2(2), SPATC1(2), KRTAP19-5(2), MITF(2), NAP1L1(2), RSBN1L(2), ZKSCAN4(2), FYB2(2), ARL4C(2), FOCAD(2), INSC(2), C2orf80(2), ZBED6CL(2), BLOC1S3(2), ANKRD34B(2), GJB5(2), SLC35E2B(2), PLEKHG4(2), SFTA2(2), NOXO1(2), GUCA2A(2), FITM2(2), CCER1(2), S100A10(2), NRARP(2), DDX39B(2), SLC9A6(2), INPP5F(2), PCMTD2(2), OOEP(2), TCEA3(2), SLC44A4(2), VWA7(2), SAMD9(2), LCMT1(2), KRTAP19-8(2), CFAP99(2), EWSAT1(2), ST13P5(2), UGT2B11(2), SCART1(2), SLC6A10P(2), ARHGEF33(2), MS4A4E(2), C16orf90(2), PEX26(2), ATAD3C(2), POM121L12(2), BTBD19(2), ETDB(2), SPANXB1(2), TEX46(2), USP17L1(2), ZNF826P(2), HLA-DPA1(2), ZBTB22(2), CKMT1B(2), TMEM250(2), TXNDC5(2), KIR3DL3(2), C4orf48(2), GSTA1(2), TMEM225B(2), PCDHA11(2), ATP6V1E2(2), TAF11L14(2), LSM14A(2), AL096870.1(2), MRC1(2), AC026954.2(2), ANXA8(2), AC004223.3(2), ZNF723(2), ZNF728(2), SLC25A53(2), SSX4B(2), C17orf50(2), AL603832.3(2), AL024498.2(2), LINC01138(2), ZNF280B(2), PRSS2(2), AK2(1), AP2B1(1), CAMK1G(1), CSDE1(1), CD22(1), TACC3(1), ISL1(1), CHDH(1), GLT8D1(1), RUFY3(1), CD74(1), PRKCH(1), TRIO(1), CTPS2(1), MCUR1(1), PHF21B(1), PRKCQ(1), ASPM(1), PRR11(1), GUCY2C(1), DGCR2(1), WIPI1(1), TCF3(1), ADGRL1(1), CACNG4(1), ATP12A(1), ZCWPW1(1), PCM1(1), UBE2D4(1), SCGN(1), DNAJA1(1), NME8(1), HSD17B14(1), BAX(1), SLC4A11(1), RCOR1(1), UPRT(1), CRISP3(1), SCD(1), CATSPERG(1), GSTT2(1), YPEL1(1), NEFH(1), APOBEC3H(1), TTLL12(1), TAB1(1), APOL1(1), COCH(1), SNW1(1), DHRS7(1), RPS6KA5(1), C14orf93(1), DHRS2(1), BMP7(1), FERMT1(1), KLF5(1), CCDC113(1), AAGAB(1), RIPK2(1), EIF3E(1), TULP2(1), PIH1D1(1), PPP6R1(1), PLIN3(1), CDC37(1), HAS1(1), PRPF31(1), UPK1A(1), ETHE1(1), RUNDC3B(1), OGDH(1), ANKRD7(1), PRUNE2(1), CASC3(1), CHRNE(1), PSMD11(1), KRT32(1), CNTNAP1(1), DUSP3(1), HLF(1), TMEM97(1), FOXN1(1), SLAIN2(1), UGT2B10(1), ZNF330(1), TBC1D19(1), ELP4(1), CRTAM(1), APOC3(1), ALDH2(1), SPRING1(1), C12orf57(1), TREML2(1), SLC22A2(1), SMOC2(1), CCN6(1), NNT(1), TFG(1), NCBP2(1), SLC41A3(1), IL1A(1), STEAP3(1), TTC31(1), STK25(1), SLC1A4(1), PARD3B(1), CEP104(1), RAP1A(1), FBXO2(1), C1orf21(1), MPL(1), CHRNB4(1), KIF14(1), DDX59(1), CA14(1), DENND1A(1), TTLL2(1), PLXDC2(1), WASHC3(1), CRISPLD1(1), TMIGD3(1), POLM(1), SLC25A16(1), HVCN1(1), ITPR2(1), EEF1AKMT3(1), H2BW1(1), BATF3(1), HMGB1P1(1), PCK1(1), EFNB2(1), TEKT3(1), MIF4GD(1), CD70(1), CST8(1), HECTD3(1), CCR7(1), RHOJ(1), CRYGN(1), ALDH1A2(1), NDUFA10(1), TEX101(1), NINJ1(1), PEX11B(1), USP29(1), RAF1(1), RGS22(1), FCRL2(1), FBXO44(1), CHI3L1(1), CCNA1(1), MYH11(1), MBD2(1), CCNB1(1), DSC2(1), DSC1(1), BIVM(1), UGT2B28(1), KCP(1), NT5E(1), PRPH(1), ZC3H10(1), KIAA0513(1), MRPL44(1), VILL(1), CHAD(1), GH2(1), TOR1A(1), ARHGEF39(1), KIF13A(1), TINAG(1), STRA6(1), BCAR3(1), BRDT(1), CYP2C8(1), OIT3(1), NAAA(1), COL2A1(1), FRMD6(1), FANCI(1), MAP1LC3B(1), SECTM1(1), MBD1(1), SOD1(1), SYTL1(1), RGL1(1), OSR1(1), HNRNPLL(1), RPS27A(1), LIPT1(1), GRIP2(1), NFKBIZ(1), UGT3A1(1), MTFR2(1), OGT(1), CETN2(1), PRDM14(1), CDKN2B(1), GLYAT(1), LYPD1(1), DOCK1(1), UEVLD(1), ATP6V1G3(1), MEPE(1), RPIA(1), CEP112(1), EPHB1(1), VOPP1(1), PIP4P2(1), PPM1J(1), SETD9(1), FZD7(1), MICU3(1), N6AMT1(1), TSPAN7(1), FUT6(1), PPP2R2B(1), TBC1D31(1), ARMC12(1), DYRK1A(1), GALNT14(1), CD1B(1), COPG2(1), AC005041.1(1), SIM2(1), IRX6(1), NAE1(1), PIP(1), ZNF222(1), IQCC(1), SPC24(1), SPATA17(1), FCMR(1), FCAMR(1), MSX1(1), CDC42EP3(1), PBXIP1(1), SPTA1(1), ATXN7(1), FYCO1(1), C1orf50(1), ZNF691(1), SPRY1(1), TMEM155(1), TMEM174(1), SFXN1(1), ZNF704(1), GBX1(1), PIGA(1), ZCCHC24(1), ZNF22(1), TMEM52B(1), TMX3(1), CCDC68(1), NYAP1(1), ACSF2(1), URM1(1), GOLGA6C(1), NIBAN3(1), SPATA33(1), C19orf33(1), ATG16L2(1), FADD(1), LMBRD1(1), DEGS2(1), ARF4(1), BDKRB2(1), FEN1(1), FAM178B(1), CHTF8(1), COL4A3(1), UMOD(1), RNASE3(1), PCDH7(1), TM4SF4(1), NIPA1(1), VGLL2(1), CNGB3(1), LONRF2(1), LSM3(1), MUC7(1), JUNB(1), CHD7(1), KCND3(1), TBCA(1), PIK3CD(1), GPHN(1), FBXL14(1), FBXW10(1), EIF2AK3(1), ISG20(1), ATOH1(1), C1QTNF4(1), CTSW(1), PSMD1(1), WFIKKN2(1), ATP2A2(1), MYO1H(1), CHST2(1), PCSK1(1), UBQLNL(1), CCDC85B(1), NUPR1(1), RIMS2(1), VPS37D(1), DCAF4L2(1), FMR1NB(1), TEX44(1), LMO7DN(1), TMEM52(1), TMEM139(1), SELENOW(1), FJX1(1), LYNX1(1), HCLS1(1), TMEM64(1), OR5T1(1), USH1G(1), DEXI(1), P2RY8(1), UBE2E2(1), KCNJ14(1), OTOL1(1), SATB1(1), MAFA(1), GLUD2(1), CCDC60(1), IZUMO1R(1), NOG(1), FIGLA(1), NPIPA5(1), KCNJ12(1), SERINC4(1), B3GALT5-AS1(1), LSAMP(1), SPATA8(1), IFIT1(1), DMWD(1), ZNF829(1), NBPF6(1), RGS7BP(1), MIR22HG(1), C17orf58(1), BCR(1), LUZP2(1), DPPA3(1), SAMD11(1), CCDC157(1), AD000671.1(1), ZNF669(1), FAM83G(1), ASTL(1), HACD4(1), H1-0(1), STK40(1), CPNE4(1), ASB13(1), ZNF140(1), NBPF4(1), SLC30A10(1), PIWIL2(1), ZNF98(1), FBXL22(1), PIGN(1), STPG3(1), FAM118B(1), NBEAP2(1), ZNF560(1), NUP62CL(1), KRTAP4-1(1), PAPSS2(1), GPATCH3(1), ALPK2(1), PRC1(1), MAP3K3(1), DMD(1), RBM20(1), HSD17B8(1), TMEM235(1), HSPA1B(1), PRAMEF14(1), C6orf15(1), MUC21(1), DEFB121(1), DHX16(1), MIR1915HG(1), TRIM27(1), MALRD1(1), TTC25(1), PCDHGA1(1), PABPN1L(1), AC105052.1(1), CNEP1R1(1), CCDC85C(1), ARRDC5(1), KRTAP20-4(1), KRTAP2-3(1), KRTAP3-1(1), SULT1A4(1), FAM209B(1), MAGEB1(1), ZSWIM7(1), RPL17-C18orf32(1), SYCE3(1), PPP2R2A(1), FADS3(1), OR2A1(1), HSBP1L1(1), ERVMER34-1(1), DHFR(1), PRPS1L1(1), AC011005.1(1), TMEM253(1), TSPY4(1), H2BS1(1), KBTBD13(1), PCDHA13(1), MRPS17(1), PCDHGC5(1), EGFL8(1), SERPINB10(1), ELFN2(1), LINC01011(1), CLRN2(1), FER1L5(1), HS3ST5(1), LRRC37BP1(1), PCDHA12(1), HOXA10(1), EIF5AL1(1), EEF1G(1), SYS1-DBNDD2(1), AP002373.1(1), ZNF10(1), AP002748.5(1), AL513165.2(1), MAP1LC3B2(1), RTEL1(1), SPECC1L-ADORA2A(1), AL162231.3(1), ZHX1-C8orf76(1), UBE2Q2L(1), SLC22A31(1), HSPB9(1), AC010542.3(1), HPR(1), RBM8A(1), AC008687.1(1), AC008403.1(1), AC003002.2(1), HSFX2(1), H3Y2(1), TRABD2B(1), FBXO17(1), AC010422.6(1), MTRNR2L6(1), H2AC19(1), AL353588.1(1), F8A3(1), SRCIN1(1), TBC1D3E(1), FP565260.4(1)

5.4 Best C-index test in all runs

Best Elastic Net model (C-Index test)

[INFO] Coefs. list

[1] “ABAT, ABCC2, AC233723.1, AC245033.1, ACSL3, ACSM5, AKT1S1, ANGPTL4, ANO4, AQP8, BEX4, BEX5, BTN2A2, C1QTNF6, CAMTA1, CLEC17A, CPA2, CPXM2, CR2, CRYGD, CTSL, DKK1, DSG2, DTNBP1, EPHX1, FAM83A, FLNC, FRZB, FUT4, GALNT2, GOLGA6D, GPD1L, HERPUD1, HLA-DOB, JOSD1, KIR3DL2, KRT6A, LDLRAD3, MARCHF4, MELTF, NOS3, NPAS2, NTSR1, NUMBL, PITX3, PLEKHB1, PZP, RHOF, RPE65, SEPTIN2, SERBP1, SLC46A3, SLC4A8, SQLE, STAP1, STOX1, TFDP1, TLE1, TM4SF19, VAX1”

Test set

Full set

Best Hub model (C-Index test)

[INFO] Coefs. list

[1] “ABL1, AC005726.1, ACO2, ACTA1, ACTBL2, ACTC1, ACTL6B, ACTL7B, ACTL8, ACTR3B, ACTRT3, AKT1, AKT2, ALB, ANKRD53, AP000311.1, CALB2, CALM3, CD79A, CDC42, CDK15, CDK4, CDK5, CDY2B, CFTR, CPS1, CRYGD, DECR1, EEF1E1-BLOC1S5, EP300, EPHA6, EPHA7, FGFR1, FURIN, FYN, GAPDH, GATA4, GLI2, GLI3, GMPS, GSK3A, HSPA2, HSPA4, HSPA8, INSR, KAT8, LCK, MAPK1, MAPK11, MAPK12, MAPK13, MRAS, MYO18B, NFKB1, NME8, NOS3, NRAS, OAS2, OAS3, OASL, PCSK9, PIK3CG, PITX3, POTEJ, PRDM10, PRKACB, PRKAR1A, PRKCA, PRKCD, PSKH2, RAB11A, RAC1, RAC3, RAD23B, RB1, RHOF, RHOQ, RHOV, RPS6KA1, RRAS, SIRT1, SLC2A4, SMAD3, SRC, SST, STK11, TNF, TOMM34, TSPO, TSPY1, TSPY3, TYRO3, UBA52, UBC, UBL4B, UMPS, VEGFA, WT1, YES1, YWHAE, ZFAND4, ZNF479”

Test set

Full set

Best Orphan model (C-Index test)

[INFO] Coefs. list

[1] “ENSG00000021300, ENSG00000035720, ENSG00000088543, ENSG00000100558, ENSG00000102409, ENSG00000102445, ENSG00000110900, ENSG00000112308, ENSG00000114638, ENSG00000117477, ENSG00000120211, ENSG00000121236, ENSG00000124466, ENSG00000124508, ENSG00000125498, ENSG00000125775, ENSG00000128298, ENSG00000133466, ENSG00000134297, ENSG00000134827, ENSG00000142621, ENSG00000145107, ENSG00000147689, ENSG00000148704, ENSG00000161055, ENSG00000161714, ENSG00000163975, ENSG00000164794, ENSG00000165730, ENSG00000166448, ENSG00000166669, ENSG00000166845, ENSG00000171357, ENSG00000171360, ENSG00000172155, ENSG00000175664, ENSG00000175874, ENSG00000176029, ENSG00000179397, ENSG00000179709, ENSG00000183044, ENSG00000187912, ENSG00000188483, ENSG00000188910, ENSG00000189431, ENSG00000197062, ENSG00000198208, ENSG00000198788, ENSG00000198967, ENSG00000203943, ENSG00000206077, ENSG00000206531, ENSG00000224916, ENSG00000240403, ENSG00000251349, ENSG00000259330, ENSG00000262481, ENSG00000269179, ENSG00000276085, ENSG00000280071, ENSG00000280969”

Test set

Full set

5.5 Best Log-rank test in all runs

Best Elastic net (Log-rank test)

[INFO] Coefs. list

[1] “ABAT, ABCC2, AC245033.1, ACTC1, ADM, AHSG, AKT1S1, ANGPTL4, ANKRD65, ANP32A, AP000311.1, AP3S1, BEX4, CALB2, CBFA2T3, CCDC149, CCDC88C, CD200R1L, CDKAL1, CERS4, CIDEC, CLEC17A, CLEC20A, CPXM2, CRYGD, DKK1, DNAJB4, DTNBP1, E2F7, ELMO2, ENPP5, ENTPD1, EPHX1, FAM83A, FBN2, FDXACB1, FLNC, GALNT2, GNG7, GOLGA6D, GPD1L, GPR1, GUCA2B, HOXA13, INSL4, IRX5, ISL2, KCNG1, KIR2DL1, KIR3DL2, KLHDC8B, KRT38, KRT6A, KYNU, LCE5A, LDLRAD3, LINGO2, MELTF, MTHFS, MYO6, NEIL3, NGRN, OR14C36, PLEKHB1, POPDC3, PRORY, RASSF10, RCVRN, RGS20, RHCG, RHOF, RHOV, RPS6KL1, RUBCNL, SETDB2, SLC46A3, SOWAHC, SPANXA1, STAP1, STIMATE, TDRD1, TEX26, TLE1, TMEM130, TRPA1, TSPY3, TXLNB, UQCRB, USP4, UTS2, VAX1, VDAC1, WFDC3, WWC2-AS2, ZBTB18, ZNF479, ZNF502”

Test set

Full set

Best Hub model (Log-rank test)

[INFO] Coefs. list

[1] “ABL1, AC005726.1, ACTA1, ACTA2, ACTBL2, ACTC1, ACTL6B, ACTL8, ACTR1B, ACTR2, ACTRT3, AKT1, ANKRD53, AP000311.1, ARG2, ARL14, AURKC, CALB2, CALM2, CALN1, CD79A, CDC42, CDH1, CDK15, CDK4, DECR1, DIRAS1, EHMT2, EPHA1, FGF2, FGF8, FURIN, FUT4, FYN, GAPDH, GATA4, GCG, GLI2, GSK3A, HRAS, HSPA4, HSPA8, INS, KIT, KLF10, KRAS, LATS2, LCK, LEF1, LGR4, LINGO2, MAP3K19, MAPK11, MAPK12, MAPK13, MAPK4, MAPK7, MRAS, MYBL1, MYC, MYH14, NEDD4, NFKBIA, NOS3, NOTCH1, NRAS, OASL, PIK3CG, PIM2, PITX3, POTEJ, PPP3CA, PPP3CC, PRKACB, PRKCA, PRKCD, PRKX, PSKH2, RAB25, RAC1, RAD23B, RHOF, RHOQ, RHOV, RIPK4, RIT2, RPS6KA1, RRAS, SEPTIN2, SPANXA1, SRC, STK11, TF, TFRC, TGFB1, TLE1, TNFRSF11A, TP53, TSPO, TTC16, TYRO3, UBC, UBD, UBL4B, UMPS, VAX1, VEGFA, WT1, YES1, ZFAND4, ZNF165, ZNF479”

Test set

Full set

Best Orphan model (Log-rank test)

[INFO] Coefs. list

[1] “AC005697.1, AC010325.1, ADRA2B, AKT1S1, BEX4, BEX5, BTN2A2, C19orf48, C1QL2, C1QTNF6, C20orf141, C3orf18, CA5B, CCDC149, CDIN1, CIDEC, CLEC17A, DBP, DNAJC28, EFCAB8, EMC6, ENSG00000270168, FAM210B, FAM83A, GATD3B, GNG7, GOLGA6D, HHIPL2, HSDL1, IER5L, KIR2DL1, KIR3DL2, KLHDC8B, KRT38, KRT6A, LDLRAD3, LURAP1, MELTF, MSLNL, MYLIP, NEIL3, NRG4, OLFM1, PEDS1, PLCD3, PLEKHA8P1, PLEKHB1, PRAMEF1, SLC46A3, STAP1, TCP10L2, TM4SF19, TMEM130, UCN2, UPK1B, VAX1, ZNF750, ZSCAN26”

Test set

Full set

NULL

6 Parameters for the report

## [INFO]          balanced.sets: TRUE
## [INFO]        calc.params.old: FALSE
## [INFO]           coding.genes: TRUE
## [INFO]     degree.correlation: pearson
## [INFO]          degree.cutoff:       0.000
## [INFO]            degree.type: string
## [INFO]      degree.unweighted: TRUE
## [INFO]      handle.duplicates: keep_first
## [INFO]                   log2: TRUE
## [INFO]                n.cores:      14.000
## [INFO]          normalization: center
## [INFO]                 ntimes:    5000.000
## [INFO]                project: luad.data.2018.10.17
## [INFO]                   seed:    1985.000
## [INFO]                 subset: Inf
## [INFO]   subtract.surv.column: (I do not know how to display this)
## [INFO]            target.vars: list(alpha = 0.1, vars = 110), list(alpha = 0.1, vars = 56), list(alpha = 0.1, vars = 97)
## [INFO]                 tissue: primary.solid.tumor
## [INFO]                  train:       0.800